Exam 1: Biochem

Question 1

Compare the predominating interactions of the different amino acid R groups

Answer 1

Nonpolar aliphatic and aromatic R groups: Van der Waal’s interactions; hydrophobic and associate with the interior of amino acids

Sulfur-containing R groups: can form disulfide bonds

Polar, uncharged R groups: Hydrogen binding

Charged R groups: electrostatic interactions

Question 2

When pKa of an ionizable group equals the pH in its environment, which form dominates?

Answer 2

HA and A- exist in equilibrium.

Question 3

When the pH of an environment is more basic than the pKa of an ionizable group, which form of that group dominates?

Answer 3

The A- form.

Question 4

When the pH of an environment is more acidic than the pKa of an ionizable group, which form dominates?

Answer 4

The HA form.

Question 5

What is the pKa of carboxylic acid?

Answer 5

Between 2-4

Question 6

What is the pKa of an amine group?

Answer 6

Approximately 9.

Question 7

Describe endocrine signaling.

Answer 7

In endocrine signaling, ligands travel relatively long distances via the bloodstream. The ligand may be hormones (small molecules or proteins secreted by glands) or cytokines (small proteins secreted by non-glands, usually have immunomodulating function).

Question 8

Describe autocrine signaling.

Answer 8

A cell releases a signal and responds to the ligand itself. This is important in tissue growth, organ development, immune response and inflammatory response.

Question 9

Describe paracrine signaling.

Answer 9

A cell releases a signal that travels a short distance to its neighbor. Think synaptic signaling.

Question 10

A cell secretes a ligand and the downstream effect is that 1,000s of proteins are modified. This is an example of what important quality of cell signal transduction?

Answer 10

Amplification.

Question 11

Hormone X with a really intimidating name binds with endohoohahlongname receptor and triggers a bunch of intermediate functions that don’t matter, resulting in the tissue of the kidney responding one way to the ligand and the tissue of the liver responding a different way. This is an example of what important quality of cell signal transduction?

Answer 11

Microheterogeneity. The same ligand can elicit different (coordinated) responses with a cell, or different cells may respond differently to the same ligand (often due to isozymes*).

Question 12

What is the most important difference between an agonist and an antagonist?

Answer 12

An agonist initiates a signaling cascade. An antagonist does not, and competitively or noncompetitively inhibit agonists.

Question 13

List 5 common effector enzymes.

Answer 13

Kinases, lipases, phosphotases, binding facilitators, nucleotidyl cyclases (convert ATP>cAMP or GTP>cGMP).

Question 14

List 4 common second messengers.

Answer 14

Ip3, Ca+2, DAG, cAMP.

Question 15

3 important things that must occur for signal to be terminated:

Answer 15

1. ) Ligand/receptor complex must be inactivated;
2. ) intermediates (effector proteins, second messengers) must be lost (either degraded or diffuse away);
3. ) Target protein must return to original state.

Question 16

Receptor X is a GPCR that binds with hormone Y and triggers a signaling cascade. This cascade activates adenylyl cyclase. A mutation in receptor X causes endogenous molecule Z to covalently bond to the receptor.
Describe molecule Z in terms of its relationship to hormone Y.
What is the result of this mutation?

Answer 16

Molecule Z is an irreversible antagonist.

The result of the mutation is decreased activity of adenylyl cylcase, which converts ATP>cAMP, so low [cAMP] will result (since cAMP activates PKA, reduced PKA activity would also result).

**I made this all up so it might not be realistic, but I wanted a scenario to keep these concepts all straight! :)

Question 17

In a typical RTK cascade, which protein has GTPase activity?

Answer 17

RAS.

Question 18

A 65-year-old woman suffering from atrial fibrillation had been taking a drug to treat this condition for 6 months. The drug had no intrinsic activity and bound reversibly to β1 receptors. What term best defines this drug?

Answer 18

Because the drug has no intrinsic activity, we can assume it is an antagonist.

Because it binds reversibly, we know it is a competitor.

Therefore, it can be described as a competitive antagonist.

Question 19

The thyroid is stimulated to release thyroid hormone by thyroid stimulating hormone (TSH), which is produced by the pituitary gland and transported by the bloodstream. This type of hormonal signaling is called:

Answer 19

Endocrine.

Question 20

The insulin receptor is a tyrosine kinase receptor. When insulin binds hepatic insulin receptors, a pathway that activates cAMP phosphodiesterase is stimulated. Which of the following events will most likely occur in hepatocytes in response to increased serum insulin levels?

Answer 20

When cAMP phosphodiesterase is stimulated, cAMP will be degraded.

One function of cAMP is to activate PKA, so if [cAMP] is reduced, PKA activity will decrease.

Question 21

Are the charges on carboxyl, amino, and side chain groups of amino acids universal?

Answer 21

No, they depend on pH of environment.

At physiological pH (7.4), the amino acid is positively charged and the carboxyl group is negatively charged.

Question 22

What determines the formation of a-helicies and b-sheets?

Answer 22

Backbone interactions (so primary structure). R groups do not affect formation of these structures.

Question 23

What fundamentally determines protein folding?

Answer 23

Primary structure.

Question 24

What determines tertiary structure?

Answer 24

The interactions of side chains (ex: electrostatic interactions, Van der Waal’s forces, etc).

Question 25

What might denature a protein?

Answer 25

High temps, high or low pH, mutations or modifications that are destabilizing (such as b-pleated sheet formation - from Dr. McCarthy’s problems), solvents.

Question 26

What is a function of protein disulfide isomerase?

Answer 26

Helps facilitate protein folding (heat-shock protein also does this).

Question 27

What is the difference between AL amyloidosis and AB amyloidosis?

Answer 27

AL: often affects kidneys (but can involve any tissue); proteins from immunoglobin light chains involved.
AB: deposition of beta-amyloid into the tissues of the brain (Alzheimer’s).

Question 28

Explain AGEs and their effect on tissue function.

Answer 28

AGE = advanced glycosylation end products.

High [glucose] can result in the nonenzymatic glycosylation of proteins. This in itself does not necessarily denature the protein (see “suggested problems”) but the subsequent oxidation and cross-linking CAN cause misfolding, creating large, nonfunctional protein aggregates, which interfere with tissue function.

Question 29

You want to prescribe a patient a drug that would be contraindicated in someone with reduced cardiac function. Your patient tells you that she has never had a heart attack, but does say that she had an “episode” three months ago of tightness in the chest, shortness of breath, and radiating pain. She “chalked it up to stress”. What test could be ordered to help decide if this patient is a candidate for this drug?

Answer 29

Measuring levels of cardiac tissue-specific isozymes in the blood could help you be sure if the event was an MI or not: (ex: troponin), as it should only reside in the heart, and would be released into systemic circulation only with damage to cardiac tissue.

Question 30

What is the difference between an isozyme specific to the liver and an isozyme specific to the kidney?

Answer 30

Isozymes have moderately different primary and tertiary structures, but the same function.

Question 31

A lower Km means lower or higher affinity for substrate?

Answer 31

Higher affinity.

Question 32

When Km = [S], what is Vi equal to?

Answer 32

Half of Vmax.

Question 33

A sigmoidal kinetic plot indicates what?

Answer 33

Cooperative binding; an allosteric effector is present.

Sigmoidal curves also have steeper slopes than hyperbolic curves; if so, they are more sensitive to [S].

Question 34

Compare the effects of competitive, noncompetitive, and mixed inhibitors on the Vmax and Km when introduced to an agonist.

Answer 34

Competitive: Vmax can be reached; Km shifts up (right).

Noncompetitive: Cannot reach Vmax. Km shifts down (left).

Mixed: Cannot reach Vmax. Km can shift either way.

Question 35

Compare heteroallosteric and homoallosteric enzymes.

Answer 35

A homoallosteric enzyme adopts a different conformation in response to binding its substrate, allowing it to bind more of that substrate at different sites (=cooperative substrate binding). Hemoglobin binds one oxygen, making it easier to bind more oxygen.

A heteroallosteric enzyme undergoes a conformational change in response to binding a positive and/or negative regulator at a regulatory site.

**Please edit if this isn’t accurate or clear. I’m not 100% on the difference between these.

Question 36

What do positive and negative regulators do?

Answer 36

Both bind heteroallosteric enzymes and modulate the enzyme’s activity.

Positive increase enzymatic activity. This decreases Km.

Negative reduce enzymatic activity (example: a CYP inhibitor?). This increases Km.

Vmax usually remains the same when a positive or negative regulator is introduced to cooperative binding.

Question 37

What is the most common reversible covalent modification, how is it achieved, and how is it reversed?

Answer 37

Phosphorylation by protein kinases, and is undone by protein phosphatases.

Question 38

Explain proteolytic cleavage.

Answer 38

An inactive protein (a “zygomen”) is cleaved by a proteolytic protein and thus activated. This is an irreversible process.

This is the case with digestive proteases, for example, which would be problematic running around the body in the active form (because they would digest stuff inappropriately). Proproteins also undergo proteolytic cleavage.

Question 39

What is the difference between a heteroallosteric receptor bound to a negative regulator and an enzyme bound to an inhibitor?

Answer 39

The negative regulator will decrease affinity to the substrate (increase Km) while the inhibitor reduces activity of the enzyme.